Two Companies one legal entity

We are set up with a single legal entity that has multiple companies for which I need to produce different AP Checks.  I have created a new organization for the second company, a new payment process profile tied to the check format for that company.  Now, I am unsure how to ensure that when I submit a payment request, i only get the invocies that pertain to that company in the check run.  I thought at my last job that we used pay groups to segregate the companies but I am not seeing that as an option in the payment